tests/testthat/_snaps/lefse.md

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

lefse output of oxygen

Code
  mm_lefse
Output
  microbiomeMarker-class inherited from phyloseq-class
  normalization method:              [ CPM ]
  microbiome marker identity method: [ lefse ]
  marker_table() Marker Table:       [ 12 microbiome markers with 5 variables ]
  otu_table()    OTU Table:          [ 276 taxa and  177 samples ]
  sample_data()  Sample Data:        [ 177 samples by  71 sample variables ]
  tax_table()    Taxonomy Table:     [ 276 taxa by 1 taxonomic ranks ]

Code
  marker_table(mm_lefse)
Output
                                                                                                                                 feature
  marker1                                                    k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae
  marker2                                k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Faecalibacterium
  marker3        k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Faecalibacterium|s__Faecalibacterium_s__
  marker4                                                                                        k__Bacteria|p__Firmicutes|c__Clostridia
  marker5                                                                       k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales
  marker6                             k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcaceae_g__
  marker7  k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcaceae_g__|s__Ruminococcaceae_g___s__
  marker8                                                                                           k__Bacteria|p__Firmicutes|c__Bacilli
  marker9                                                                        k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales
  marker10             k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_s__
  marker11                                                   k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae
  marker12                                  k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus
           enrich_group   ef_lda       pvalue         padj
  marker1       Healthy 4.993303 7.154793e-05 7.154793e-05
  marker2       Healthy 4.832765 5.914547e-04 5.914547e-04
  marker3       Healthy 4.830757 6.043983e-04 6.043983e-04
  marker4       Healthy 4.648541 7.176046e-04 7.176046e-04
  marker5       Healthy 4.648541 7.176046e-04 7.176046e-04
  marker6       Healthy 4.317335 6.990210e-03 6.990210e-03
  marker7       Healthy 4.317335 6.990210e-03 6.990210e-03
  marker8         Tumor 4.648541 7.176046e-04 7.176046e-04
  marker9         Tumor 4.514859 3.267911e-03 3.267911e-03
  marker10        Tumor 4.211031 4.371742e-03 4.371742e-03
  marker11        Tumor 4.122063 4.724670e-03 4.724670e-03
  marker12        Tumor 4.121855 4.812008e-03 4.812008e-03

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.